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Lysine acetylation in human fecal microbiome

ABSTRACT: This study characterized the lysine acetylome in human gut microbiome samples. Briefly, the microbial peptides obtained from human mcirobiome cells were used for lysine acetylated peptide enrichment using anti-acetyl-lysine (Kac) antibody cocktail; the enriched Kac peptides were then identified and quantified using mass spectrometry.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Human Gut Metagenome

TISSUE(S): Bacterial Protein

SUBMITTER: Xu Zhang

LAB HEAD: Daniel Figeys

PROVIDER: PXD015482 | Pride | 2020-07-08

REPOSITORIES: Pride

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Widespread protein lysine acetylation in gut microbiome and its alterations in patients with Crohn's disease.

Zhang Xu X Ning Zhibin Z Mayne Janice J Yang Yidai Y Deeke Shelley A SA Walker Krystal K Farnsworth Charles L CL Stokes Matthew P MP Couture Jean-François JF Mack David D Stintzi Alain A Figeys Daniel D

Nature communications 20200817 1

Lysine acetylation (Kac), an abundant post-translational modification (PTM) in prokaryotes, regulates various microbial metabolic pathways. However, no studies have examined protein Kac at the microbiome level, and it remains unknown whether Kac level is altered in patient microbiomes. Herein, we use a peptide immuno-affinity enrichment strategy coupled with mass spectrometry to characterize protein Kac in the microbiome, which successfully identifies 35,200 Kac peptides from microbial or human ...[more]

PMID: 32807798

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Lysine acetylation of microbiome

Project description:This project study and comprehensively characterize the lysine acetyltion in the human gut microbiome using antibody-based enrichment strategry and Orbitrap mass spectrometer. The technique has also been applied to study the microbiome in pediatric Crohn's disease and control subjects in order to understand the functional alterations of microbiome in IBD.

2020-07-08 | PXD013427 | Pride

Extracellular vesicles isolated from the descending colon of pediatric patients with inflammatory bowel disease and control patients

Project description:Characterizing the proteomic profile of extracellular vesicles isolated from the descending colon of pediatric patients with inflammatory bowel disease and control participants

2018-09-11 | PXD007959 | Pride

Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification

Project description:We report the identification of 67 previously undescribed histone modifications, increasing the current number of known histone marks by about 70%. We further investigated one of the marks, lysine crotonylation (Kcr), confirming that it represents an evolutionarily-conserved histone posttranslational modification. The unique structure and genomic localization of histone Kcr suggest that it is mechanistically and functionally different from histone lysine acetylation (Kac). Specifically, in both human somatic and mouse male germ cell genomes, histone Kcr marks either active promoters or potential enhancers. In male germinal cells immediately following meiosis, Kcr is enriched on sex chromosomes and specifically marks testis-specific genes, including a significant proportion of X-linked genes that escape sex chromosome inactivation in haploid cells. These results therefore dramatically extend the repertoire of histone PTM sites and designate Kcr as a specific mark of active sex chromosome-linked genes in postmeiotic male germ cells. 2 histone marks (pan-lysine acetylation and pan-lysine crotonylation) were studied in 1 human cell type and 2 mouse cell types using ChIP-Seq. Input was sequenced for each cell type as a control. Pan-anti_Kac and pan-anti_Kcr antibodies were custom developed with PTM BioLab, Co., Ltd (Chicago, IL).

2011-10-06 | E-GEOD-32663 | biostudies-arrayexpress

Effects of BAFASAL on human microbiome

Project description:This project aims to examinw the effects of an anti-Salmonella bacteriophage preparation, BAFASAL, on ex vivo human gut microbiome composition and function using a multi-omics approach

2022-02-17 | PXD027172 | Pride

The acetylome analysis of lysine acetylation in the plant pathogenic bacterium Brenneria nigrifluens

Project description:Protein lysine acetylation, a dynamic and reversible posttranslational modification, plays a crucial role in several cellular processes including cell cycle regulation, metabolic pathways, enzymatic activities and protein interactions. Brenneria nigrifluens is the pathogen of shallow bark canker of walnut trees and can cause serious disease on walnut trees. Up to now, it is little known about the roles of lysine acetylation in the plant pathogenic bacteria. In the present study, the lysine acetylome of B. nigrifluens was determined by high-resolution LC-MS/MS analysis. In total, we identified 1,866 lysine acetylation sites distributed in 737 acetylated proteins. Bioinformatics results indicate that acetylated proteins participate in many different biological functions in B. nigrifluens. Four conserved motifs, namely, LKac, Kac*F, I*Kac and L*Kac, were identified in this bacterium. Protein interaction network analysis indicates that all kinds of interactions are modulated by protein lysine acetylation. Overall, 14 acetylated proteins are related to the virulence of B. nigrifluens.

2019-09-30 | PXD014046 | Pride

First proteomic analysis of lysine acetylation on extensive functions in Solenopsis invicta Buren

Project description:Lysine acetylation (Kac) plays a critical role in the regulation of a great deal of important cellular processes. However, little is known about Kac in Solenopsis invicta, which is one of the 100 most dangerous invasive species in the world. Lysine acetylome in S. invicta was evaluated for the first time in this study. Altogether, 2387 Kac sites were tested in 992 proteins. The prediction of subcellular localization indicated that most identified proteins were located in cytoplasm, mitochondria and nucleus. The enriched Kac site motifs included Kac H, Kac Y, Kac G, Kac F, Kac T, and Kac W. H, Y, F, and W were of frequent occurrence at the +1 position, whereas G, Y and T were of frequent occurrence at the –1 position. Based on cellular component, acetylated proteins were enriched in cytoplasmic part, mitochondrial matrix, and cytosolic ribosome. Furthermore, 25 pathways were detected to be significantly enriched. Interestingly, arginine and proline metabolism as well asphagosome, which were related to immunity, contained several Kac proteins. Acetylation or deacetylation of the proline and phagosome proteins may adjust the protein function, which may be why S. invicta was highly immune. As for interaction network investigation, diverse interactions were adjusted by Kac. Our study of lysine acetylome supplies abundant information for function analysis of reversible Kac in the growth and development of S. invicta and other Hymenoptera insects. Confirming the functions of Kac target proteins may be useful to design specific and effective drugs to prevent and control this dangerous invasive species.

2020-12-02 | PXD019033 | Pride

Protein acetylation landscape of developing rice anthers

Project description:Protein lysine acetylation (KAC) is a dynamic and reversible post-translational modification, playing important biological roles in many organisms.Here, we reported results from a proteomic investigation to detect KAC status of the developing rice anthers near the time of meiosis (RAM), providing strong biochemical evidence for roles of many KAC-affected proteins during rice anther development and meiosis. We identified a total of 1,354 KAC sites in 676 proteins.

2019-03-06 | PXD007986 | Pride

Rice (Oryza sativa) lysine-acetylation LC-MS/MS

Project description:Lysine acetylation is a dynamic and reversible post-translational modification that plays an imporant role in the gene transcription regulation. Here, we report high quality proteome-scale data for lysine-acetylation sites and proteins in rice (Oryza sativa). A total of 1337 Kac sites in 716 Kac proteins with diverse biological functions and subcellular localizations were identified in rice seedlings.

2016-02-24 | PXD002291 | Pride

A complex containing lysine-acetylated actin inhibits the formin INF2

Project description:INF2 is a member of the formin family of actin assembly factors. Dominant mis-sense mutations in INF2 link to two diseases: focal segmental glomerulosclerosis (FSGS), a kidney disease; and Charcot-Marie-Tooth disease (CMTD), a neuropathy. All disease mutations map to the autoinhibitory Diaphanous Inhibitory Domain (DID). Curiously, purified INF2 is not autoinhibited, suggesting the existence of additional cellular inhibitors. We purified an INF2 inhibitor from mouse brain, and identified it as a complex between lysine-acetylated actin (KAc-actin) and cyclase-associated protein (CAP). Inhibition of INF2 by CAP/KAc-actin requires INF2 DID. Treatment of CAP/KAc-actin with histone deacetylase 6 (HDAC6) releases INF2 inhibition, while HDAC6 inhibitors block cellular INF2 activation. INF2 disease mutants are poorly inhibited by CAP/KAc-actin, suggesting that FSGS and CMTD result from reduced CAP/KAc-actin binding. This is the first demonstrated role for lysine-acetylated actin: regulation of an actin assembly factor by a novel mechanism, which we call facilitated auto-inhibition.

2018-07-18 | MSV000082634 | MassIVE

Proteomic analysis of lysine acetylation provides strong evidence for involvement of acetylated histone and chloroplast proteins in CWMV infected plant

Project description:Protein lysine acetylation (Kac) is an important post-translational modification (PTM) mechanism in both eukaryotes and prokaryotes, with key roles in cellular regulation. To investigate the role of Kac in plants infected with virus, we characterized the lysine acetylome of Nicotiana benthamiana plants with or without a Chinese Wheat Mosaic Virus (CWMV) infection by using TMT labeling-based protein modification differential analysis, high-resolution liquid chromatography mass spectrometry analysis, and integrated bioinformatics analysis. Here, we identified 4803 acetylated lysine sites on 1964 proteins. A comparison of the acetylation levels of the CWMV-infected group with those of the uninfected group revealed that 747 sites were up-regulated on 422 proteins, including chloroplast localization proteins and histone H3, and 150 sites were down-regulated on 102 proteins when using a change threshold of at least 1.2 times and a t-test p-value of <0.05. Nineteen conserved motifs were extracted; 51% of the identified proteins were localized to the chloroplast. Among the acetylated proteins, 19 Kac sites were combined in core histones, including 10 Kac sites on histone 3. Bioinformatics analysis revealed that Kac occurs on a diverse range of proteins involved in a wide variety of biological processes, especially photosynthesis. Furthermore, we demonstrate that the acetylation level of chloroplast localization proteins and histone H3 are significantly increased. In summary, our results reveal the regulatory roles of Kac in response to CWMV infection.

2021-05-07 | PXD012537 | Pride

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